@article{bowtie,
        author = {Langmead, B. and Trapnell, C. and Pop, M. and Salzberg, S.},
    journal = {Genome Biology},
    number = {3},
    pages = {R25--10},
    title = {{Ultrafast and memory-efficient alignment of short {DNA} sequences to the human genome}},
    volume = {10},
    year = {2009}
}


@article{BH,
    author = {Benjamini, Y. and Hochberg, Y.},
    journal = {Journal of the Royal Statistical Society. Series B (Methodological)},
    number = {1},
    pages = {289--300},
    title = {{Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing}},
    volume = {57},
    year = {1995}
}

@article{USeq, title={Empirical methods for controlling false positives and estimating confidence in {ChIP-Seq} peaks}, volume={9}, number={1}, journal={BMC Bioinformatics}, publisher={BioMed Central}, author={Nix, D. A. and Courdy, S. J. and Boucher, K. M.}, year={2008}, pages={523}}

@article{Chen2012Systematic,
    author = {Chen, Yiwen and Negre, Nicolas and Li, Qunhua and Mieczkowska, Joanna O. and Slattery, Matthew and Liu, Tao and Zhang, Yong and Kim, Tae-Kyung and He, Housheng H. and Zieba, Jennifer and Ruan, Yijun and Bickel, Peter J. and Myers, Richard M. and Wold, Barbara J. and White, Kevin P. and Lieb, Jason D. and Liu, X. Shirley},
      journal = {Nature Methods},
    posted-at = {2012-04-23 20:01:43},
    title = {{Systematic evaluation of factors influencing ChIP-seq fidelity}},
    volume = {advance online publication},
    year = {2012}
}


@article{Roy2010, title={{Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE}}, volume={330}, url={http://www.sciencemag.org/content/330/6012/1787.abstract}, number={6012}, journal={Science}, author={Roy, Sushmita and Ernst, Jason and Kharchenko, Peter V and Kheradpour, Pouya and Negre, Nicolas and Eaton, Matthew L and Landolin, Jane M and Bristow, Christopher A and Ma, Lijia and Lin, Michael F and et al., {with modENCODE Consortium}}, year={2010}, pages={1787--1797}}

@article{Wu11, title={{Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration}}, volume={21}, url={http://www.ncbi.nlm.nih.gov/pubmed/21795386}, number={10}, journal={Genome Research}, publisher={COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT}, author={Wu, W. and Cheng, Y. and Keller, C.  A. and Ernst, J. and Kumar, S. A. and Mishra, T. and Morrissey, C. and Dorman, C. M and Chen, K-B. and Drautz, D. and et al.}, year={2011}, pages={1659--1671}}

@article{Storey03, title={{The positive false discovery rate: A Bayesian interpretation and the q-value}}, volume={31}, url={http://www.jstor.org/stable/3448445}, number={6}, journal={Annals of Statistics}, publisher={JSTOR}, author={Storey, J. D.}, year={2003}, pages={2013--2035}}

@article{Liang12,
author = {K. Liang and S. Kele\c{s}},
title = {Normalization of {ChIP}-seq Data with Control},
year = {2012},
journal= {BMC Bioinformatics},
number = {13},
volume = {199},
note= {Published online 2012 August 10. doi:  10.1186/1471-2105-13-199}
}




@article{Xu10, title={A signal-noise model for significance analysis of {ChIP-seq} with negative control.}, volume={26}, url={http://www.ncbi.nlm.nih.gov/pubmed/20371496}, number={9}, journal={Bioinformatics}, publisher={Oxford Univ Press}, author={Xu, H. and Handoko, L. and Wei, X. and Ye, C. and Sheng, J. and Wei, C-L. and Lin, F. and Sung, W-K.}, year={2010}, pages={1199--204}}

@article{Kuan11, title={A Statistical Framework for the Analysis of {ChIP-Seq} Data}, volume={106}, url={http://pubs.amstat.org/doi/abs/10.1198/jasa.2011.ap09706}, number={495}, journal={Journal of the American Statistical Association}, publisher={American Statistical Association}, author={Kuan, P. F. and Chung, D. and Pan, G. and Thomson, J. A. and Stewart, R. and Kele\c{s}, S.}, year={2011}, pages={891--903}}

@ARTICLE{Ji08,
  AUTHOR =       {H. Ji and H. Jiang and W. Ma and D. S. Johnson and R. M. Myers and W. H. Wong},
  TITLE =        {An integrated software system for analyzing {ChIP}-chip and {ChIP}-seq data},
  JOURNAL =      {Nature Biotechnology},
  YEAR =         {2008},
  volume =       {26},
  number =       {},
  pages =        {1293-1300},
  month =        {},
  note =         {},
  abstract =     {},
  keywords =     {},
  source =       {},
}


@ARTICLE{Zhang08,
  AUTHOR =       {Y. Zhang and T. Liu and C. A. Meyer and J. Eeckhoute and D. S. Johnson and B. E. Bernstein and C. Nussbaum and R. M. Myers and M. Brown and W. Li and X. S. Liu},
    TITLE =        {Model-based Analysis of {ChIP-Seq (MACS)}},
  JOURNAL =      {Genome Biology},
  YEAR =         {2008},
  volume =       {9},
  number =       {9},
  pages =        {R137},
  month =        {},
  note =         {},
  abstract =     {},
  keywords =     {},
  source =       {},
}

@article{Park09, title={{ChIP-seq}: advantages and challenges of a maturing technology.}, volume={10}, url={http://www.ncbi.nlm.nih.gov/pubmed/19736561}, number={10}, journal={Nature Reviews Genetics}, publisher={Nature Publishing Group}, author={Park, P. J.}, year={2009}, pages={669--80}}

@ARTICLE{Rozowsky09,
  AUTHOR =       {J. Rozowsky and G. Euskirchen and R. Auerbach and D. Zhang and T. Gibson and R. Bjornson and N. Carriero and M. Snyder and M. Gerstein},
    TITLE =       {{PeakSeq enables systematic scoring of ChIP-Seq experiments relative to controls}},
  JOURNAL =      {Nature Biotechnology},
  YEAR =         {2009},
  volume =       {27},
  number =       {1},
  pages =        {66-75},
  month =        {},
  note =         {},
  abstract =     {},
  keywords =     {},
  source =       {},
}


@Article{Kharchenko08,
author = {P. V. Kharchenko and  M. Tolstorukov and P. J. Park},
title = {Design and analysis of {C}h{IP}-seq experiments for {DNA}-binding proteins},
journal = {Nature Biotechnology},
year = {2008},
volume = {6},
pages = {1351-1359}
}

@Article{Hoetal2011,
AUTHOR = {Ho, Joshua and Bishop, Eric and Karchenko, Peter and Negre, Nicolas and White, Kevin and Park, Peter},
TITLE = {{ChIP-chip versus ChIP-seq: Lessons for experimental design and data analysis}},
JOURNAL = {BMC Genomics},
VOLUME = {12},
YEAR = {2011},
NUMBER = {1},
PAGES = {134}
}

Genome Res. September 2012 22: 1760-1774; doi:10.1101/gr.135350.111 

@Article{GENCODE,
  AUTHOR =       {Jennifer Harrow and Adam Frankish and Jose M. Gonzalez and Electra Tapanari and Mark Diekhans and Felix Kokocinski and Bronwen L. Aken and Daniel Barrell and Amonida Zadissa and Stephen Searle and If Barnes and Alexandra Bignell and Veronika Boychenko and Toby Hunt and Mike Kay and Gaurab Mukherjee and Jeena Rajan and Gloria Despacio-Reyes and Gary Saunders and Charles Steward and Rachel Harte and Michael Lin and Cédric Howald and Andrea Tanzer and Thomas Derrien and Jacqueline Chrast and Nathalie Walters and Suganthi Balasubramanian and Baikang Pei and Michael Tress and Jose Manuel Rodriguez and Iakes Ezkurdia and Jeltje van Baren and Michael Brent and David Haussler and Manolis Kellis and Alfonso Valencia and Alexandre Reymond and Mark Gerstein and Roderic Guigó and and Tim J. Hubbard},
  TITLE = {{GENCODE: The reference human genome annotation for The ENCODE Project}},
  YEAR =         {2012},
  MONTH =        {09},
  VOLUME={22},
  PAGES={1760-1774},
  journal={Genome Research}
}

@article{ENCODE2011, title={{A Userʼs Guide to the Encyclopedia of DNA Elements (ENCODE)}}, volume={9}, url={http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3079585&tool=pmcentrez&rendertype=abstract}, number={4}, journal={PLoS Biology}, publisher={Public Library of Science}, author={Myers, Richard M and Stamatoyannopoulos, John and Snyder, Michael and Dunham, Ian and Hardison, Ross C and Bernstein, Bradley E and Gingeras, Thomas R and Kent, W James and Birney, Ewan and Wold, Barbara and et al.}, editor={Becker, Peter BEditor}, year={2011}, pages={21}}

@article{McDaniell2010,
author = {R. McDaniell and B-K. Lee and L. Song and Z. Liu and A. P. Boyle and  M. R. Erdos and L.  J. Scott and M. A. Morken and K. S. Kucera and A. Battenhouse and
 D. Keefe and F. S. Collins and H. F. Willard and J. D. Lieb and T. S. Furey and G. E. Crawford and V. R. Iyer and E. Birney}, 
title = {Heritable Individual-Specific and Allele-Specific Chromatin Signatures in Humans}, 
volume = {328},
number = {5975}, 
pages = {235-239}, 
year = {2010}, 
journal = {Science} 
}

@article{wilbanks2010,
    author = {Wilbanks, E. G. and Facciotti, M. T.},
    journal = {PLoS ONE},
    publisher = {Public Library of Science},
    title = {Evaluation of Algorithm Performance in {ChIP-seq} Peak Detection},
    year = {2010},
    month = {07},
    volume = {5},
    pages = {e11471},
    number = {7},
    doi = {10.1371/journal.pone.0011471}
}        

@article{Gerstein2010,
    author = {Gerstein, M. B. and Lu, Z. J. and Van Nostrand, E. L. and Cheng, C. and Arshinoff, B. I. and Liu, T. and Yip, K. Y. and Robilotto, R. and Rechtsteiner, A. and Ikegami, K. and Alves, P. and Chateigner, A. and Perry, M. and Morris, M. and Auerbach, R. K. and Feng, X. and Leng, J. and Vielle, A. and Niu, W. and Rhrissorrakrai, K. and Agarwal, A. and Alexander, R. P. and Barber, G. and Brdlik, C. M. and Brennan, J. and Brouillet, J. J. and Carr, A. and Cheung, M-S. and Clawson, H. and Contrino, S. and Dannenberg, L. O. and Dernburg, A. F. and Desai, A. and Dick, L. and Dose, A. C. and Du, J. and Egelhofer, T. and Ercan, S. and Euskirchen, G. and Ewing, B. and Feingold, E. A. and Gassmann, R. and Good, P. J. and Green, P. and Gullier, F. and Gutwein, M. and Guyer, M. S. and Habegger, L. and Han, T. and Henikoff, J. G. and Henz, S. R. and Hinrichs, A. and Holster, H. and Hyman, T. and Iniguez, A. L. and Janette, J. and Jensen, M. and Kato, M. and Kent, W. J. and Kephart, E. and Khivansara, V. and Khurana, E. and Kim, J. K. and Kolasinska-Zwierz, P. and Lai, E. C. and Latorre, I. and Leahey, A. and Lewis, S. and Lloyd, P. and Lochovsky, L. and Lowdon, R. F. and Lubling, Y. and Lyne, R. and MacCoss, M. and Mackowiak, S. D. and Mangone, M. and McKay, S. and Mecenas, D. and Merrihew, G. and Miller, D. M. and Muroyama, A. and Murray, J. I. and Ooi, S-L. and Pham, H. and Phippen, T. and Preston, E. A. and Rajewsky, N. and Ratsch, G. and Rosenbaum, H. and Rozowsky, J. and Rutherford, K. and Ruzanov, P. and Sarov, M. and Sasidharan, R. and Sboner, A. and Scheid, P. and Segal, E. and Shin, H. and Shou, C. and Slack, F. J. and Slightam, C. and Smith, R. and Spencer, W. C. and Stinson, E. O. and Taing, S. and Takasaki, T. and Vafeados, D. and Voronina, K. and Wang, G. and Washington, N. L. and Whittle, C. M. and Wu, B. and Yan, K-K. and Zeller, G. and Zha, Z. and Zhong, M. and Zhou, X. and modENCODE Consortium and Ahringer, J. and Strome, S. and Gunsalus, K. C. and Micklem, G. and Liu, X. S. and Reinke, V. and Kim, S. K. and Hillier, L. W. and Henikoff, S. and Piano, F. and Snyder, M. and Stein, L. and Lieb, J. D. and Waterston, R. H.}, 
    title = {Integrative Analysis of the {Caenorhabditis elegans} Genome by the {modENCODE} Project}, 
    volume = {330}, 
    number = {6012}, 
    pages = {1775-1787}, 
    year = {2010},
    journal = {Science} 
}

@article{Kasowski2010,
author = {Kasowski, M. and Grubert, F. and Heffelfinger, C. and Hariharan, M. and Asabere, A. and Waszak, S. M. and Habegger, L. and Rozowsky, J. and Shi, M. and Urban, A.  E. and Hong, M-Y. and Karczewski, K. J. and Huber, W. and Weissman, S. M. and Gerstein, M. B. and Korbel, J. O. and Snyder, M.}, 
title = {Variation in Transcription Factor Binding Among Humans}, 
volume = {328}, 
number = {5975}, 
pages = {232-235}, 
year = {2010},
journal = {Science} 
}

@MISC{1000Genomes,
  author =       "1000 Genomes Project",
  title =        "{The 1000 Genomes Project}",
  howpublished = "",
  year =         "",
  month =        "",
  note =         "\texttt{http://www.1000genomes.org/page.php}",
  abstract =     "",
  keywords =     "",
  source =       "",
  file = F
}



@MISC{RoadmapEpigenome,
  author =       "RoadmapEpigenome",
  title =        "{The NIH Roadmap Epigenomics Mapping Consortium}",
  howpublished = "",
  year =         "",
  month =        "",
  note =         "\texttt{http://www.roadmapepigenomics.org/}",
  abstract =     "",
  keywords =     "",
  source =       "",
  file = F
}

@MISC{HapMap,
  author =       "HapMap",
  title =        " International HapMap Project",
  howpublished = "",
  year =         "",
  month =        "",
  note =         "\texttt{http://hapmap.ncbi.nlm.nih.gov/}",
  abstract =     "",
  keywords =     "",
  source =       "",
  file = F
}
@MISC{modENCODE,
  author =       "modENCODE",
  title =        "mod{ENCODE}: {M}odel {O}rganism {ENC}yclopedia {O}f {DNA} {E}lements ",
  howpublished = "",
  year =         "",
  month =        "",
  note =         "\texttt{http://www.modencode.org/}",
  abstract =     "",
  keywords =     "",
  source =       "",
  file = F
}

@article{Parr1980,
author = {Parr, W.C. and Schucany, W.R.}, 
title = {Minimum distance and robust estimation}, 
volume = {75}, 
number = {371}, 
pages = {616-624}, 
year = {1980},
journal = {Journal of the American Statistical Association} 
}



@Unpublished{FNR,
author={K. Myers and H. Yan and I. Ong and D. Chung and K. Liang and F. Tran and S. Keles and R. Landick and P. Kiley},
title={Genome-scale Analysis of \textit{{E}. coli} {FNR} Reveals the Complexity of Bacterial Regulon Structure},
note={Under revision in \textit{Molecular Systems Biology}},
year={2012}
}

@article{ENCODE,
author={{The ENCODE Project Consortium}},
title={An integrated encyclopedia of {DNA} elements in the human genome},
journal={Nature},
volume={489},
pages={57-74},
month={09},
year={2012},
date={06}
}

@article{PICS,
title={Probabilistic Inference for {ChIP-seq}},
author={X. Zhang and G. Robertson and M. Krzywinski and K. Ning and A. Droit and S. Jones and R. Gottardo},
journal={Biometrics},
volume={67},
issue={1},
month={03},
year={2011},
pages={151–163}
}

@article{ZINBA,
author={Rashid, N. and Giresi, P. and Sun, W. and Ibrahim, J. and Lieb, J.},
title={{ZINBA} integrates local covariates with {DNA}-seq data to identify broad and narrow regions of enrichment, even within amplified genomic regions},
journal={Genome Biology},
year={2011},
volume={12},
pages={R67}
}


@Unpublished{zuo12,
author = {Zuo, C. and Kele\c{s}, S.},
title = {A Statistical Framework for Power Calculations in{ ChIP-seq} Experiments},
note = {Submitted},
month = {December},
year = {2012}
}



@Manual{mosaics,
    title = {mosaics: {MOSAiCS (MOdel-based one and two Sample Analysis and Inference for ChIP-Seq)}},
    author = {D. Chung and P-F. Kuan and S. Kele\c{s}},
    year = {2012},
    note = {R package version 1.4.1. \url{http://groups.google.com/group/mosaics_user_group}, \url{http://bioconductor.org/packages/2.11/bioc/html/mosaics.html}}
  }

@Manual{spp,
    title = {spp: some description},
    author = {P. Kharchenko},
    year = {2008},
    note = {R package version 1.0. \url{http://compbio.med.harvard.edu/Supplements/ChIP-seq/spp_1.0.tar.gz}}
  }


